Willus,
With your help, now I can extract any pages from the secure pdf file. And the overlapping functionality is useful too. Unfortunately, the cbox option does not work for me, as instead of selecting a region, I need to cut out and discard a region. And another complication is that the book is not produced by computer originally, but with traditional metal typeface publishing method. Thus the page design is not very accurate and the rectangular regions I need to cut-out do not overlay, and each lines do not overlay either. So any batch processing does not work well.
So far, for trial method, I followed the following steps:
(1) With k2pdfopt, I generated a copy of the original secure pdf, getting rid of its security.
(2) With pdfsam, I splitted the book into single pages.
(3) For each single page, I used cbox option to divided a page into 2 pages, namely top page and buttom page.
(4) For the top page, I used again cbox to divided it into left and right portion, discarded the unnecessary part (the boxed original text part)
(5) Before I merge back the top and buttom part, I need to resize the top part's width to the buttom part's width. Otherwise, as portion of the top part was cut out, they have different width and thus reflowing does not work well.
(6) Merged the top and buttom part into a single pdf page.
(7) With pdfsam again, merged all pages into one pdf file.
(8) Used k2pdfopt to reflow.
This is just for around 10-20 pages for trial, as the manual workload is too much.
I attached the overlayed odd and even pages.